SED-ML, publications and model databases. Many Figures in journal publications cannot easily be reproduced by the curators of model databases and later end-users. The Figure shows how SED-ML can help model curators in reproducing simulations submitted together with a manuscript. A workflow for the publication process would involve the following steps: 1, a researcher submits a manuscript with a mathematical model to a scientific journal; 2, the manuscript is sent out for scientific review; the researcher can submit his model directly to a model database such as BioModels Database or JWS Online, either concurrently with step 1 or via the journal office. 3, Model curators perform a technical curation of the model, (i.e. check whether the model description is complete, whether the model can be simulated and whether the results shown in the manuscript can be reproduced); 4, if the model passes the technical curation it could be made available for the scientific reviewer on a secure site (as it is the case for instance with JWS Online); 5, after scientific review the manuscript might become acceptable and published; 6, after which readers can access the manuscript; and 7, the model is moved to the public database, and is accessible for simulation. SED-ML would greatly facilitate steps 3, 4, and 7."
Waltemath et al. BMC Systems Biology 2011 5:198 doi:10.1186/1752-0509-5-198